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US20100086501A1 - Determining Age Ranges of Skin Samples - Google Patents

Determining Age Ranges of Skin Samples Download PDF

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Publication number
US20100086501A1
US20100086501A1 US12/550,060 US55006009A US2010086501A1 US 20100086501 A1 US20100086501 A1 US 20100086501A1 US 55006009 A US55006009 A US 55006009A US 2010086501 A1 US2010086501 A1 US 2010086501A1
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skin
sample
nucleic acid
subject
protein
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Sherman H. Chang
Gail K. Naughton
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Dermtech International
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Dermtech International
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Publication of US20100086501A1 publication Critical patent/US20100086501A1/en
Priority to US14/715,424 priority patent/US20150259739A1/en
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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61Q—SPECIFIC USE OF COSMETICS OR SIMILAR TOILETRY PREPARATIONS
    • A61Q17/00—Barrier preparations; Preparations brought into direct contact with the skin for affording protection against external influences, e.g. sunlight, X-rays or other harmful rays, corrosive materials, bacteria or insect stings
    • A61Q17/04—Topical preparations for affording protection against sunlight or other radiation; Topical sun tanning preparations
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61Q—SPECIFIC USE OF COSMETICS OR SIMILAR TOILETRY PREPARATIONS
    • A61Q19/00—Preparations for care of the skin
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61Q—SPECIFIC USE OF COSMETICS OR SIMILAR TOILETRY PREPARATIONS
    • A61Q19/00—Preparations for care of the skin
    • A61Q19/08—Anti-ageing preparations
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/5308—Immunoassay; Biospecific binding assay; Materials therefor for analytes not provided for elsewhere, e.g. nucleic acids, uric acid, worms, mites
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/68—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids
    • G01N33/6881—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids from skin
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/148—Screening for cosmetic compounds
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/156—Polymorphic or mutational markers
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/158—Expression markers
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2500/00—Screening for compounds of potential therapeutic value
    • G01N2500/04—Screening involving studying the effect of compounds C directly on molecule A (e.g. C are potential ligands for a receptor A, or potential substrates for an enzyme A)
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2800/00—Detection or diagnosis of diseases
    • G01N2800/20—Dermatological disorders

Definitions

  • the present invention relates generally to skin sampling and more specifically to methods of characterizing skin based on an age index.
  • Aging is the accumulation of changes in an organism or object over time. Aging in humans refers to a multidimensional process of physical, psychological, and social change. Some dimensions of aging grow and expand over time, while others decline. Reaction time, for example, may slow with age, while knowledge of world events and wisdom may expand. Research shows that even late in life potential exists for physical, mental, and social growth and development. Aging is an important part of all human societies reflecting the biological changes that occur, but also reflecting cultural and societal conventions.
  • Human skin is a complex organ which extends over the entire body. There are different types of skin at different portions of the body; for example, facial skin is different from that of the scalp, and even the skin on the front (palm) of the hand is different than that on the back of the hand.
  • skin is generally composed of two main layers of tissue.
  • the epidermis or cuticle the outermost layer, is composed of superficial layers (from the outside in: stratum corneum, stratum lucidem, and stratum granulosum) and deep layers (stratum spinosum and stratum basale).
  • the dermis, cutis vera, or the true skin is composed of a papillary layer above and a reticular layer below.
  • senescence is the state or process of aging.
  • Cellular senescence is a phenomenon where isolated cells demonstrate a limited ability to divide in culture (i.e., the Hayflick Limit, discovered by Leonard Hayflick in 1965), while “Organismal senescence” is the aging of organisms. After a period of near perfect renewal (in humans, between about 20 and 35 years of age), organismal senescence is characterized by the declining ability to respond to stress, increasing homeostatic imbalance and increased risk of disease. This irreversible series of changes inevitably ends in death. Some researchers (specifically biogerontologists) are treating aging as a disease. As genes that have an effect on aging are discovered, aging is increasingly being regarded in a similar fashion to other genetic conditions, i.e., potentially “treatable.”
  • the present invention is based, in part, on the discovery that analysis of nucleic acids or protein products from specific genes can be used to distinguish or categorize skin samples of individuals.
  • the methods provide valuable genetic information based on DNA, RNA, or protein products obtained therefrom, for example.
  • the method involves use of a non-invasive approach for recovering nucleic acids such as DNA or RNA or proteins from the surface of skin via a tape stripping procedure that permits a direct quantitative and qualitative assessment of biomarkers.
  • a non-invasive approach for recovering nucleic acids such as DNA or RNA or proteins from the surface of skin via a tape stripping procedure that permits a direct quantitative and qualitative assessment of biomarkers.
  • tape-harvested nucleic acid and protein products are shown to be comparable in quality and utility to recovering such molecules by biopsy
  • the non-invasive method provides information regarding cells of the outermost layers of the skin that may not be obtained using biopsy samples.
  • the non-invasive method is far less traumatic than a biopsy, although the invention does not exclude the use of such invasive methods for skin sampling.
  • the method is used to capture cells on the skin of individuals for determination of the appropriate age range.
  • Nucleic acid molecules obtained from skin are analyzed in order to characterize the skin sample as being young or old.
  • a nucleic acid molecule is amplified prior to analysis. Secondary outcomes could include tests for diagnosis and prognosis of a variety of symptoms of photoaging and/or chronoaging of skin, and to predict a therapeutic or cosmetic regimen for treating the skin.
  • the skin cells are lysed to extract one or more proteins, which are then quantitated to compare with gene products of the genes listed in Table 1, Table 2, Table 3, or any combination thereof, for example, however, the combination must include at least one “young” gene and at least “old” gene.
  • non-invasive techniques as described herein for obtaining skin samples.
  • one of skill in the art would know other techniques for obtaining a skin sample such as scraping of the skin, biopsy, suction, blowing and other techniques.
  • non-invasive tape stripping as described in U.S. Pat. No. 6,949,338, incorporated herein by reference, is an illustrative example for obtaining a skin sample.
  • the methods involve detection of one or more mutations in the nucleic acid sequence of the nucleic acid molecule obtained from the skin.
  • mutations may be a substitution, a deletion, and/or an insertion of the nucleic acid sequence that results in symptoms associated with chronoaging and/or photoaging of skin from the subject from which the skin sample is obtained.
  • the nucleic acid analyzed is any one or more of those listed in Table 1, Table 2, Table 3, or any combination thereof. Accordingly, provided herein is a method for determining the age range of a skin sample of a subject, including obtaining a nucleic acid or protein by tape stripping or biopsy of the skin or a skin lesion, for example, from the subject, and analyzing the nucleic acid as compared to the nucleic acids or protein products thereof listed in Table 1, Table 2, Table 3, or any combination thereof. In this method, at least one nucleic acid molecule whose expression is informative of an appropriate age range of the skin is detected in the sample.
  • the non-invasive methods of the invention involve applying an adhesive tape to a target area of skin in a manner sufficient to isolate a sample adhering to the adhesive tape, wherein the sample includes nucleic acid molecules and/or proteins. Typically, at least one nucleic acid molecule or protein whose expression is informative of the age or age range of the skin in the sample.
  • the method of characterizing skin using tape stripping has a number of applications, such as the following: (i) age classification of the skin; (ii) monitoring the severity and progression of photoaging and/or chronoaging; (iii) monitoring treatment efficacy; and (iv) prediction of a particular treatment or cosmetic regimen.
  • non-polar, pliable, adhesive tapes especially pliable tapes with rubber adhesive
  • pliable tapes with rubber adhesive are more effective than other types of adhesive tapes.
  • pliable tapes with rubber adhesives as few as 10 or less tape strippings and in certain examples as few as 4 or even 1 tape stripping can be used to isolate and/or detect nucleic acid molecules from the epidermal layer of the skin.
  • the methods of the invention provide for determining the age range of a skin sample or of skin in situ, including application of a detectably labeled probe directly to the skin of a subject for visual analysis. At least one nucleic acid molecule whose expression is informative of the age range of the skin is detected on the skin using a specific probe. In one example, expression of one or more of the genes listed in Table 1, Table 2, Table 3, or any combination thereof is detected on the skin to determine the age range of the skin. In one embodiment, expression of one or more of the genes listed in Table 1, Table 2, Table 3, or any combination thereof is detected in the sample to characterize the skin sample.
  • the invention provides kits for characterizing a skin sample in a subject.
  • the kit includes a skin sample collection device, such as a biopsy needle or an adhesive tape for non-invasive tape stripping, and one or more probes or primers that selectively bind to one or more nucleic acid molecules in Table 1, Table 2, Table 3, or any combination thereof, or to a nucleic acid or protein expression product of a nucleic acid molecule in Table 1, Table 2, Table 3, or any combination thereof.
  • the kit may include one or more pairs of forward primers that selectively bind upstream of a gene on one strand and reverse primers that selectively bind upstream of a gene on a complementary strand.
  • the kit includes a microarray containing at least a fragment of a gene or a nucleic acid or protein product of a gene identified in Table 1, Table 2, Table 3, or any combination thereof, or any combination thereof.
  • the kit for characterizing a skin sample from a subject includes an applicator and one or more probes or primers that selectively bind to one or more nucleic acid molecules in Table 1, Table 2, Table 3, or any combination thereof, or to a nucleic acid or protein expression product of a nucleic acid molecule in Table 1, Table 2, Table 3, or any combination thereof.
  • the probes are detectably labeled for visual identification of expression of RNA.
  • the invention provides a cosmetic formulation containing agents for reducing or increasing expression of genes.
  • the agent reduce or increase expression of the genes listed in Table 1, Table 2, Table 3, or any combination thereof.
  • the cosmetic formulation is an emulsion, a cream, a lotion, a solution, an anhydrous base, a paste, a powder, a gel, or an ointment.
  • the emulsion may be an oil-in-water emulsion or a water-in-oil emulsion.
  • the formulation may be a solution, such as an aqueous solution or a hydro-alcoholic solution.
  • the cosmetic formulation is an anhydrous base, such as a lipstick or a powder.
  • the formulation is comprised within an anti-aging product or a moisturizing product.
  • the cosmetic formulation may further contain one or more of estradiol; progesterone; pregnanalone; coenzyme Q10; methylsolanomethane (MSM); copper peptide (copper extract); plankton extract (phytosome); glycolic acid; kojic acid; ascorbyl palmitate; all trans retinol; azaleic acid; salicylic acid; broparoestrol; estrone; adrostenedione; androstanediols; or sunblocks.
  • FIG. 1 is a hierarchial cluster analysis of the identified 100-gene classifier distinguishing skin samples of young individuals from skin samples of old individuals.
  • the tree configuration shown at the left of the cluster analysis is representative of the genes in the order as shown in Table 1.
  • FIG. 2 is a graphical diagram showing a skin age index generated from the 100-gene classifier that distinguishes skin samples of young individuals from skin samples of old individuals.
  • FIG. 3 is a hierarchial cluster analysis of the identified 61-gene classifier distinguishing skin samples of young individuals from skin samples of old individuals.
  • Skin age index Sum of “Group A” ⁇ Sum of “group B”+ ⁇ (constant).
  • the tree configuration shown at the left of the cluster analysis is representative of the genes in the order as shown in Table 2.
  • FIG. 4 is a graphical diagram showing a skin age index generated from the 61-gene classifier that distinguishes skin samples of young individuals from skin samples of old individuals.
  • FIG. 5 is a hierarchial cluster analysis of an 83-gene classifier distinguishing skin samples of young individuals from skin samples of old individuals.
  • Skin age index Sum of “Group A” ⁇ Sum of “group B”+ ⁇ (constant).
  • the tree configuration shown at the left of the cluster analysis is representative of the genes in the order as shown in Table 3.
  • FIG. 6 is a graphical diagram showing a skin age index generated from the 83-gene classifier that distinguishes skin samples of young individuals from skin samples of old individuals.
  • the present invention is based, in part, on the discovery that analysis of nucleic acid molecules or protein products from specific genes can be used to characterize skin samples from individuals based on an age index. Accordingly, the present invention provides methods and kits useful for characterizing a skin sample based on determining an expression profile of the sample based on identification of one or more genes or proteins.
  • telomere length is maintained in immortal cells (e.g., germ cells and keratinocyte stem cells, but not other skin cell types) by the enzyme telomerase.
  • immortal cells e.g., germ cells and keratinocyte stem cells, but not other skin cell types
  • mortal cell lines can be immortalized by the activation of their telomerase gene, present in all cells but active in few cell types.
  • model organisms ranging from the simple budding yeast Saccharomyces cerevisiae to worms such as Caenorhabditis elegans and fruit flies ( Drosophila melanogaster ). Study of these organisms has revealed the presence of at least two conserved aging pathways.
  • Sir2 is required for genomic silencing at three loci: the yeast mating loci, the telomeres and the ribosomal DNA (rDNA).
  • rDNA ribosomal DNA
  • yeast replicative aging may be partially caused by homologous recombination between rDNA repeats; excision of rDNA repeats results in the formation of extrachromosomal rDNA circles (ERCs).
  • ERCs extrachromosomal rDNA circles
  • ERCs have not been observed in other species of yeast (which also display replicative senescence), and ERCs are not believed to contribute to aging in higher organisms such as humans.
  • Extrachromosomal circular DNA eccDNA
  • worms, flies and humans The role of eccDNA in aging, if any, is unknown.
  • SIRT1 can also regulate acetylates such as CBP/p300, and has been shown to deacetylate specific histone residues.
  • RAS1 and RAS2 also affect aging in yeast and have a human homologue. RAS2 overexpression has been shown to extend lifespan in yeast.
  • Superoxide dismutase a protein that protects against the effects of mitochondrial free radicals, can extend yeast lifespan in stationary phase when overexpressed.
  • aging is likely to be regulated in part through the insulin/IGF-1 pathway. Mutations that affect insulin-like signaling in worms, flies and mice are associated with extended lifespan.
  • PNC1 is transcriptionally upregulated under stressful conditions such as caloric restriction, heat shock, and osmotic shock. By converting nicotinamide to niacin, it removes nicotinamide, which inhibits the activity of Sir2.
  • a nicotinamidase found in humans, known as PBEF may serve a similar function, and a secreted form of PBEF known as visfatin may help to regulate serum insulin levels. It is not known, however, whether these mechanisms also exist in humans since there are obvious differences in biology between humans and model organisms.
  • Sir2 activity has been shown to increase under calorie restriction. Due to the lack of available glucose in the cells more NAD+ is available and can activate Sir2. Resveratrol, a polyphenol found in the skin of red grapes, was reported to extend the lifespan of yeast, worms, and flies. It has been shown to activate Sir2 and therefore mimics the effects of calorie restriction.
  • the particularly important causes of chronological aging of human skin likely vary among a population of elderly humans, including such factors as diet, genetics, and environment.
  • chronological skin aging is due to activation of the stress-activated pathways (SAPs) and a repression of the mitogen-activated pathways (ERK).
  • SAPs stress-activated pathways
  • ERK mitogen-activated pathways
  • chronoaging and photoaging of human skin have a similar molecular pathophysiology. ERK mediates the actions of growth factors necessary for healthy skin. Interference with ERK can lead to thinning of chronologically-aged skin because of reduced number of cells in the epidermis and dermis.
  • SAPs activate factors (e.g., c-Jun) that promote both inhibition of procollagen synthesis and degradation of mature collagen, and thereby lead to reduced form, strength, and function of skin.
  • Chronological aging of skin might be expected to include some interference with ERK and/or some activation of the SAPs.
  • Gene expression is imperfectly controlled, and it is possible that random fluctuations in the expression levels of many genes contribute to the aging process as suggested by a study of such genes in yeast.
  • Individual cells which are genetically identical, none-the-less can have substantially different responses to outside stimuli, and markedly different lifespans, indicating the epigenetic factors play an important role in gene expression and aging as well as genetic factors.
  • the present invention employs a non-invasive tape stripping technology to obtain samples of skin from individuals.
  • DNA microarray assays are used to create a skin age index to predict the aging of an individual.
  • Tape-stripping removes superficial cells from the surface of the skin as well as adnexal cells. Small amounts of nucleic acid molecules isolated from tape-stripped cells can be amplified and used for microarray analyses and quantitative PCR. In addition, proteins obtained from the lysed cells may be quantitated for characterization and determination of age. Consequently, tape-stripping is a non-invasive diagnostic method, which does not interfere with subsequent histological analyses.
  • the present invention demonstrates that stratum corneum RNA, harvested by tape stripping with Epidermal Genetic Information Retrieval (EGIR) (see U.S. Pat. No. 6,949,338, incorporated herein by reference), can be used to distinguish skin samples of young individuals from skin samples of old individuals.
  • EGIR Epidermal Genetic Information Retrieval
  • subject refers to any individual or patient to which the subject methods are performed.
  • the subject is human, although as will be appreciated by those in the art, the subject may be an animal.
  • animals including mammals such as rodents (including mice, rats, hamsters and guinea pigs), cats, dogs, rabbits, farm animals including cows, horses, goats, sheep, pigs, etc., and primates (including monkeys, chimpanzees, orangutans and gorillas) are included within the definition of subject.
  • sample and “biological sample” refer to any sample suitable for the methods provided by the present invention.
  • a sample of cells can be any sample, including, for example, a skin sample obtained by non-invasive tape stripping or biopsy of a subject, or a sample of the subject's bodily fluid.
  • the biological sample of the present invention is a tissue sample, e.g., a biopsy specimen such as samples from needle biopsy.
  • sample refers to any preparation derived from skin of a subject.
  • a sample of cells obtained using the non-invasive method described herein can be used to isolate nucleic acid molecules or proteins for the methods of the present invention.
  • corresponding cells refers to cells or a sample from a subject that is from the same organ and of the same type as the cells being examined.
  • the corresponding cells comprise a sample of cells obtained from a healthy individual that is age-matched or within an acceptable age range such that the sample is representative of a sample typically obtained from individuals within the range.
  • Such corresponding cells can, but need not be, from an individual that is of the same sex as the individual providing the cells being examined.
  • the term “normal sample” or “control sample” refers to any sample taken from a subject of similar species that is considered healthy and of a known age.
  • a normal/standard level of RNA denotes the level of RNA present in a sample from a subject of known age.
  • a normal level of RNA can be established by combining skin samples or cell extracts taken from normal healthy age-matched subjects and determining the level of one or more RNAs present.
  • a normal level of RNA also can be determined as an average value taken from a population of subjects that fall within a known age range. Accordingly, levels of RNA in subject and control samples can be compared with the standard values. Deviation between standard and subject values establishes the parameters for characterizing age and/or distinguishing samples based on age.
  • skin refers to the outer protective covering of the body, consisting of the epidermis (including the stratum corneum) and the underlying dermis, and is understood to include sweat and sebaceous glands, as well as hair follicle structures.
  • cutaneous can be used, and should be understood to refer generally to attributes of the skin, as appropriate to the context in which they are used.
  • the epidermis of the human skin comprises several distinct layers of skin tissue.
  • the deepest layer is the stratum basalis layer, which consists of columnar cells.
  • the overlying layer is the stratum spinosum, which is composed of polyhedral cells.
  • stratum corneum constitute the outer layer of the epidermis, the stratum corneum.
  • stratum corneum At the bottom of the stratum corneum, the cells are closely compacted and adhere to each other strongly, but higher in the stratum they become loosely packed, and eventually flake away at the surface.
  • chronoaging refers to inevitable changes that occur over time that affect the skin of a subject.
  • photoaging refers to changes to the skin of a subject over time resulting from external environmental aggressors.
  • Exemplary external aggressors include, but are not limited to UV rays, free radicals, chemicals, and toxins.
  • Exemplary symptoms of chronoaging and/or photoaging of skin include, but are not limited to, loss of firmness and elasticity, dryness, loss of sheen, and lines and wrinkles.
  • the terms “sun damage” and “environmental damage,” when used in reference to skin are used broadly to encompass any external environmental aggressors that may prematurely age the skin of a subject.
  • the term “gene” refers to a linear sequence of nucleotides along a segment of DNA that provides the coded instructions for synthesis of RNA, which, when translated into protein, leads to the expression of hereditary character.
  • skin marker or “biomarker” refers to a gene whose expression level is different between skin surface samples from individuals of distinct ages or age ranges, and skin surface samples of individuals of known age or age range. Therefore, expression of a skin marker of the invention is related to, or indicative of, the age of the subject being tested. Many statistical techniques are known in the art, which can be used to determine whether a statistically significant difference in expression is observed at a high (e.g., 90% or 95%) confidence level. As such, an increase or decrease in expression of these genes is related to and can characterize age of the subject.
  • nucleic acid molecule means DNA, RNA (e.g., messenger RNA, miRNA, etc.), single-stranded, double-stranded or triple stranded and any chemical modifications thereof. Virtually any modification of the nucleic acid is contemplated.
  • a “nucleic acid molecle” can be of almost any length, from 10, 20, 30, 40, 50, 60, 75, 100, 125, 150, 175, 200, 225, 250, 275, 300, 400, 500, 600, 700, 800, 900, 1000, 1500, 2000, 2500, 3000, 3500, 4000, 4500, 5000, 6000, 7000, 8000, 9000, 10,000, 15,000, 20,000, 30,000, 40,000, 50,000, 75,000, 100,000, 150,000, 200,000, 500,000, 1,000,000, 1,500,000, 2,000,000, 5,000,000 or even more bases in length, up to a full-length chromosomal DNA molecule.
  • the nucleic acid isolated from a sample is typically RNA.
  • miRNAs are small single stranded RNA molecules an average of 22 nucleotides long that are involved in regulating mRNA expression in diverse species including humans.
  • miRNAs regulate gene expression by binding to the 3′-untranslated regions of mRNA and catalyze either i) cleavage of the mRNA; or 2) repression of translation.
  • the regulation of gene expression by miRNAs is central to many biological processes such as cell development, differentiation, communication, and apoptosis. Recently it has been shown that miRNA are active during embryogenesis of the mouse epithelium and play a significant role in skin morphogenesis.
  • miRNAs will influence, if not completely specify the relative amounts of mRNA in particular cell types and thus determine a particular gene expression profile (i.e., a population of specific mRNAs) in different cell types.
  • a particular gene expression profile i.e., a population of specific mRNAs
  • the particular distribution of specific miRNAs in a cell will also be distinctive in different cell types.
  • determination of the miRNA profile of a tissue may be used as a tool for expression profiling of the actual mRNA population in that tissue. Accordingly, miRNA levels are useful for the purposes of characterization of a subject within an age range.
  • protein refers to at least two covalently attached amino acids, which includes proteins, polypeptides, oligopeptides and peptides.
  • a protein may be made up of naturally occurring amino acids and peptide bonds, or synthetic peptidomimetic structures.
  • amino acid or “peptide residue”, as used herein means both naturally occurring and synthetic amino acids. For example, homo-phenylalanine, citrulline and noreleucine are considered amino acids for the purposes of the invention.
  • Amino acid also includes imino acid residues such as proline and hydroxyproline.
  • the side chains may be in either the (R) or the (S) configuration.
  • a “probe” or “probe nucleic acid molecule” is a nucleic acid molecule that is at least partially single-stranded, and that is at least partially complementary, or at least partially substantially complementary, to a sequence of interest.
  • a probe can be RNA, DNA, or a combination of both RNA and DNA. It is also within the scope of the present invention to have probe nucleic acid molecules comprising nucleic acids in which the backbone sugar is other that ribose or deoxyribose. Probe nucleic acids can also be peptide nucleic acids.
  • a probe can comprise nucleolytic-activity resistant linkages or detectable labels, and can be operably linked to other moieties, for example a peptide.
  • a single-stranded nucleic acid molecule is “complementary” to another single-stranded nucleic acid molecule when it can base-pair (hybridize) with all or a portion of the other nucleic acid molecule to form a double helix (double-stranded nucleic acid molecule), based on the ability of guanine (G) to base pair with cytosine (C) and adenine (A) to base pair with thymine (T) or uridine (U).
  • G guanine
  • C cytosine
  • A adenine
  • T thymine
  • U uridine
  • the nucleotide sequence 5′-ATAC-3′ is complementary to the nucleotide sequence 5′-GTAT-3′.
  • antibody as used in this invention is meant to include intact molecules of polyclonal or monoclonal antibodies, as well as fragments thereof, such as Fab and F(ab′) 2 , Fv and SCA fragments which are capable of binding an epitopic determinant.
  • the term “specifically binds” or “specifically interacts,” when used in reference to an antibody means that an interaction of the antibody and a particular epitope has a dissociation constant of at least about 1 ⁇ 10 ⁇ 6 , generally at least about 1 ⁇ 10 ⁇ 7 , usually at least about 1 ⁇ 10 ⁇ 8 , and particularly at least about 1 ⁇ 10 ⁇ 9 or 1 ⁇ 10 ⁇ 10 or less.
  • hybridization refers to the process by which a nucleic acid strand joins with a complementary strand through base pairing.
  • Hybridization reactions can be sensitive and selective so that a particular sequence of interest can be identified even in samples in which it is present at low concentrations.
  • suitably stringent conditions can be defined by, for example, the concentrations of salt or formamide in the prehybridization and hybridization solutions, or by the hybridization temperature, and are well known in the art.
  • stringency can be increased by reducing the concentration of salt, increasing the concentration of formamide, or raising the hybridization temperature.
  • hybridization under high stringency conditions could occur in about 50% formamide at about 37° C. to 42° C.
  • Hybridization could occur under reduced stringency conditions in about 35% to 25% formamide at about 30° C. to 35° C.
  • hybridization could occur under high stringency conditions at 42° C. in 50% formamide, 5 ⁇ SSPE, 0.3% SDS, and 200 mg/ml sheared and denatured salmon sperm DNA.
  • Hybridization could occur under reduced stringency conditions as described above, but in 35% formamide at a reduced temperature of 35° C.
  • the temperature range corresponding to a particular level of stringency can be further narrowed by calculating the purine to pyrimidine ratio of the nucleic acid of interest and adjusting the temperature accordingly. Variations on the above ranges and conditions are well known in the art.
  • Mutation refers to a change in the genome with respect to the standard wild-type sequence. Mutations can be deletions, insertions, or rearrangements of nucleic acid sequences at a position in the genome, or they can be single base changes at a position in the genome, referred to as “point mutations.” Mutations can be inherited, or they can occur in one or more cells during the lifespan of an individual.
  • kit or “research kit” refers to a collection of products that are used to perform a biological research reaction, procedure, or synthesis, such as, for example, a detection, assay, separation, purification, etc., which are typically shipped together, usually within a common packaging, to an end user.
  • Samples from a tissue can be isolated by any number of means well known in the art.
  • Invasive methods for isolating a sample include, but are not limited to the use of needles or scalpels, for example during biopsies of various tissues.
  • Non-invasive methods for isolating a sample include, but are not limited to tape-stripping and skin scraping.
  • the tape stripping methods provided herein typically involve applying an adhesive tape to the skin of a subject and removing the adhesive tape from the skin of the subject one or more times.
  • the adhesive tape is applied to the skin and removed from the skin about one to ten times.
  • about ten adhesive tapes can be sequentially applied to the skin and removed from the skin.
  • an adhesive tape can be applied to and removed from a target site 10, 9, 8, 7, 6, 5, 4, 3, 2, or 1 time, and/or 10, 9, 8, 7, 6, 5, 4, 3, 2, or 1 adhesive tape can be applied to and removed from the target site.
  • the adhesive tape is applied to the skin between about one and eight times, in another example, between one and five times, and in another illustrative example the tape is applied and removed from the skin four times.
  • the rubber based adhesive can be, for example, a synthetic rubber-based adhesive.
  • the rubber based adhesive in illustrative examples, has high peel, high shear, and high tack.
  • the rubber based adhesive can have a peak force tack that is at least 25%, 50%, or 100% greater than the peak force tack of an acrylic-based tape such as D-SQUAMETM.
  • D-SQUAMETM has been found to have a peak force of 2 Newtons, wherein peak force of the rubber based adhesive used for methods provided herein, can be 4 Newtons or greater.
  • the rubber based adhesive can have adhesion that is greater than 2 times, 5 times, or 10 times that of acrylic based tape.
  • D-SQUAMETM has been found to have adhesion of 0.0006 Newton meters
  • the rubber based tape provided herein can have an adhesion of about 0.01 Newton meters using a texture analyzer.
  • the adhesive used in the methods provided herein has higher peel, shear and tack than other rubber adhesives, especially those used for medical application and Duct tape.
  • adhesive tape can be fabricated into circular discs of diameter between 10 millimeters and 100 millimeters, for example between 15 and 25 millimeters in diameter.
  • the adhesive tape can have a surface area of between about 50 mm 2 and 1000 mm 2 , between about 100 mm 2 to 500 mm 2 or about 250 mm 2 .
  • the sample may be obtained by means of an invasive procedure, such as biopsy.
  • Biopsies may be taken instead of or after tape stripping and are subjected to standard histopathologic analysis. Analysis of biopsy samples taken simultaneously with tape stripping samples may then be correlated with the data generated from one or more of analysis of selected lesion RNA samples by DNA microarray, correlation of gene expression data with histopathology, and creation of a candidate expression classifier for the skin age index.
  • biopsy refers to the removal of cells or tissues for analysis.
  • biopsy procedures There are many different types of biopsy procedures known in the art. The most common types include: (1) incisional biopsy, in which only a sample of tissue is removed; (2) excisional biopsy, in which an entire lump or suspicious area is removed; and (3) needle biopsy, in which a sample of tissue or fluid is removed with a needle.
  • incisional biopsy in which only a sample of tissue is removed
  • excisional biopsy in which an entire lump or suspicious area is removed
  • needle biopsy in which a sample of tissue or fluid is removed with a needle.
  • core biopsy When a wide needle is used, the procedure is called a core biopsy.
  • fine-needle aspiration biopsy When a thin needle is used, the procedure is called a fine-needle aspiration biopsy.
  • Other types of biopsy procedures include, but are not limited to, shave biopsy, punch biopsy, curettage biopsy, and in situ biopsy.
  • the skin sample is obtained by scraping the skin with an instrument to remove one or more nucle
  • the skin sample obtained using the tape stripping method includes, epidermal cells including cells comprising adnexal structures.
  • the sample includes predominantly epidermal cells, or even exclusively epidermal cells.
  • the epidermis consists predominantly of keratinocytes (>90%), which differentiate from the basal layer, moving outward through various layers having decreasing levels of cellular organization, to become the cornified cells of the stratum corneum layer. Renewal of the epidermis occurs every 20-30 days in uninvolved skin.
  • Other cell types present in the epidermis include melanocytes, Langerhans cells, and Merkel cells.
  • the tape stripping method of the present invention is particularly effective at isolating epidermal samples.
  • Nucleic acid molecules can also be isolated by lysing the cells and cellular material collected from the skin sample by any number of means well known to those skilled in the art. For example, a number of commercial products available for isolating polynucleotides, including but not limited to, RNeasyTM (Qiagen, Valencia, Calif.) and TriReagentTM (Molecular Research Center, Inc, Cincinnati, Ohio) can be used. The isolated polynucleotides can then be tested or assayed for particular nucleic acid sequences, including a polynucleotide encoding a cytokine. Methods of recovering a target nucleic acid molecule within a nucleic acid sample are well known in the art, and can include microarray analysis.
  • Nucleic acid molecules may be analyzed in any number of ways known in the art. For example, the presence of nucleic acid molecules can be detected by DNA-DNA or DNA-RNA hybridization or amplification using probes or fragments of the specific nucleic acid molecule. Nucleic acid amplification based assays involve the use of oligonucleotides or oligomers based on the nucleic acid sequences to detect transformants containing the specific DNA or RNA.
  • analysis of the nucleic acid molecules includes genetic analysis to determine the nucleotide sequence of a gene. Since a difference in length or sequence between DNA fragments isolated from a sample and those of known sequences are due to an insertion, deletion, or substitution of one or more nucleotides, the determination of nucleic acid sequences provides information concerning mutations resulting from environmental affects on the skin of individuals. These mutations may also include transposition or inversion and are difficult to detect by techniques other than direct sequencing. Accordingly, the methods of the present invention may be used to detect genetic mutations in one or more genes listed in Table 1, Table 2, Table 3, or any combination thereof for determination and/or characterization of the age of the subject.
  • antibodies that specifically bind to the expression products of the nucleic acid molecules of the invention may be used to characterize the skin sample of the subject.
  • the antibodies may be used with or without modification, and may be labeled by joining them, either covalently or non-covalently, with a reporter molecule.
  • Means for producing labeled hybridization or PCR probes for detecting sequences related to the nucleic acid molecules of Table 1, Table 2, Table 3, or any combination thereof include oligolabeling, nick translation, end-labeling or PCR amplification using a labeled nucleotide.
  • the nucleic acid molecules, or any fragments thereof may be cloned into a vector for the production of an mRNA probe.
  • RNA polymerase such as T7, T3, or SP6 and labeled nucleotides.
  • T7, T3, or SP6 RNA polymerase
  • Suitable reporter molecules or labels include radionuclides, enzymes, fluorescent, chemiluminescent, or chromogenic agents as well as substrates, cofactors, inhibitors, magnetic particles, and the like.
  • PCR systems usually use two amplification primers and an additional amplicon-specific, fluorogenic hybridization probe that specifically binds to a site within the amplicon.
  • the probe can include one or more fluorescence label moieties.
  • the probe can be labeled with two fluorescent dyes: 1) a 6-carboxy-fluorescein (FAM), located at the 5′-end, which serves as reporter, and 2) a 6-carboxy-tetramethyl-rhodamine (TAMRA), located at the 3′-end, which serves as a quencher.
  • FAM 6-carboxy-fluorescein
  • TAMRA 6-carboxy-tetramethyl-rhodamine
  • In situ PCR may be utilized for the direct localization and visualization of target nucleic acid molecules and may be further useful in correlating expression with chronoaging or photoaging of skin.
  • Means for producing specific hybridization probes for nucleic acid molecules of the invention include the cloning of the nucleic acid sequences into vectors for the production of mRNA probes.
  • vectors are known in the art, commercially available, and may be used to synthesize RNA probes in vitro by means of the addition of the appropriate RNA polymerases and the appropriate labeled nucleotides.
  • Hybridization probes may be labeled by a variety of reporter groups, for example, radionuclides such as 32P or 35S, or enzymatic labels, such as alkaline phosphatase coupled to the probe via avidin/biotin coupling systems, and the like.
  • a normal or standard profile for expression is established.
  • Such a standard profile may be used to develop a skin age index for comparison to test samples of individuals of unknown age.
  • Standard hybridization may be quantified by comparing the values obtained from subjects of known skin characterization or age range (e.g., from subjects falling with the range of “young” (i.e., ages of about 18-30, about 19-30, about 23-29 or about 23-42) or subjects falling within the range of “old” (i.e., ages of about 60-69 or about 46-90)).
  • Standard values obtained from such samples may be compared with values obtained from samples from subjects of known age and/or known age range. Deviation between standard and subject values is used to characterize the skin of a subject.
  • a non-invasive sampling method for the characterization of the skin of a subject.
  • a sample set of skin samples of individuals of known age is created.
  • Each sample consists of nucleic acid molecules recovered by tape stripping or biopsy sample of the superficial epidermis of the individuals of known age range.
  • a standard biopsy of the same lesion may also be performed, along with accompanying analysis and characterization. Nucleic acid molecules recovered by tape stripping the superficial epidermis of normal skin will serve as a negative control.
  • the invention provides a method of distinguishing young individuals from old individuals.
  • the method includes analyzing a nucleic acid molecule from one or more genes listed in Table 1, Table 2, Table 3, or any combination thereof.
  • the skin sample of a subject of unknown age range is assayed for expression of a large number of genes.
  • Analyzing expression includes any qualitative or quantitative method for detecting expression of a gene, many of which are known in the art.
  • the method can include analyzing expression of specific markers by measuring expression of the markers using a quantitative method, or by using a qualitative method. Non-limiting methods for analyzing polynucleotides and polypeptides are discussed below.
  • Methods of analyzing expression of a gene of the present invention can utilize a microarray, or other miniature high-throughput technology, for detecting expression of one or more gene products.
  • Quantitative measurement of expression levels using such microarrays is also known in the art, and typically involves a modified version of a traditional method for measuring expression as described herein. For example, such quantitation can be performed by measuring a phosphor image of a radioactive-labeled probe binding to a spot of a microarray, using a phosphohor imager and imaging software.
  • the nucleic acid molecule is RNA, including messenger RNA (mRNA) that is isolated from a sample from the subject.
  • mRNA messenger RNA
  • Up-regulated and down-regulated gene sets for a given disease state may be subsequently combined. The combination enables those of skill in the art to identify gene sets or panels that are unique to a given age range.
  • Such gene sets are of immense determinative and characteristic value as they can be routinely used in assays that are simpler than microarray analysis (for example “real-time” quantitative PCR). Such gene sets also provide insights into pathogenesis and targets for the design of new drugs.
  • a reference database containing a number of reference projected profiles is also created from skin samples of subjects of known age and/or age range, such as, for example, “young” (i.e., ages of about 18-30, about 19-30, about 23-29 or about 23-42) or “old” (i.e., ages of about 60-69 or about 46-90).
  • the projected profile is then compared with the reference database containing the reference projected profiles. If the projected profile of the subject matches best with the profile of a particular age range in the database, the subject is determined to have skin characteristic of an individual within the identified age range.
  • Various computer systems and software can be utilized for implementing the analytical methods of this invention and are apparent to one of skill in the art.
  • Exemplary software programs include, but are not limited to, Cluster & TreeView (Stanford, URLs: rana.lbl.gov or microarray.org), GeneCluster (MIT/Whitehead Institute, URL: MPR/GeneCluster/GeneCluster.html), Array Explorer (SpotFire Inc, URL: spotfire.com/products/scicomp.asp#SAE) and GeneSpring (Silicon Genetics Inc, URL: sigenetics.com/Products/GeneSpring/index.html) (for computer systems and software, see also U.S. Pat. No. 6,203,987, incorporated herein by reference).
  • the methods of the present invention involve in situ analysis of the skin for characterization thereof.
  • nucleic acid molecules do not need to be isolated from the subject prior to analysis.
  • detectably labeled probes are contacted with a cell or tissue of a subject for visual detection of expressed RNA to characterize the skin as discussed above.
  • the methods of the present invention can also be useful for monitoring the progression of chronoaging and/or photoaging, and for monitoring the effectiveness of one or more treatments for the symptoms of chronoaging and/or photoaging. For example, by comparing the projected profile prior to treatment with the profile after treatment.
  • the methods of the present invention can also be useful for determining an appropriate treatment regimen for a subject having a specific symptom of chronoaging and/or photoaging.
  • the methods of the invention are useful for providing a means for practicing personalized medicine, wherein treatment is tailored to a subject based on the particular characteristics of the skin of the subject.
  • the method can be practiced, for example, by first characterizing the skin of the subject, as described above.
  • the methods of the invention may be repeated on a regular basis to monitor the expression profiles of the genes of interest in the subject.
  • the results obtained from successive assays may be used to show the efficacy of treatment over a period ranging from several days to months.
  • another aspect of the invention is directed to methods for monitoring a therapeutic regimen for treating a subject having symptoms of photoaging and/or chronoaging.
  • a comparison of the expression profile or mutations in the nucleic acid sequence of the nucleic acid molecule prior to and during therapy will be indicative of the efficacy of the therapy. Therefore, one skilled in the art will be able to recognize and adjust the therapeutic approach as needed.
  • the efficacy of a therapeutic regimen for treating symptoms of photoaging and/or chronoaging can be identified by an absence of symptoms or clinical signs characteristic of the age range of the subject at the time of onset of therapy. For example, restoration of skin elasticity, reduction of wrinkles, and/or restoration of skin density may all be used to identify efficacy of a therapeutic regimen.
  • the methods of the invention can be performed on a solid support (e.g., a microtiter plate, a silicon wafer, or a glass slide), wherein cell samples and/or genes of interest are positioned such that each is delineated from each other (e.g., in wells). Any number of samples or genes (e.g., 96, 1024, 10,000, 100,000, or more) can be examined in parallel using such a method, depending on the particular support used. Where samples are positioned in an array (i.e., a defined pattern), each sample in the array can be defined by its position (e.g., using an x-y axis), thus providing an “address” for each sample.
  • a solid support e.g., a microtiter plate, a silicon wafer, or a glass slide
  • Any number of samples or genes e.g., 96, 1024, 10,000, 100,000, or more
  • each sample in the array can be defined by its position (e.g., using an x-
  • An advantage of using an addressable array format is that the method can be automated, in whole or in part, such that cell samples, reagents, genes of interest, and the like, can be dispensed to (or removed from) specified positions at desired times, and samples (or aliquots) can be monitored, for example, for expression products and/or mutations in the nucleic acid sequence of the nucleic acid molecules from any one or more of the genes listed in Table 1, Table 2, Table 3, or any combination thereof.
  • the microarray can be used to monitor the expression level of large numbers of genes simultaneously (to produce a transcript image), and to identify genetic variants, mutations and polymorphisms.
  • Polynucleotides used in the microarray may be oligonucleotides that are specific to a gene or genes of interest in which at least a fragment of the sequence is known or that are specific to one or more unidentified cDNAs which are common to a particular cell type or age range.
  • the gene of interest is examined using a computer algorithm which starts at the 5′ or more preferably at the 3′ end of the nucleotide sequence.
  • the algorithm identifies oligomers of defined length that are unique to the gene, have a GC content within a range suitable for hybridization, and lack predicted secondary structure that may interfere with hybridization. In certain situations it may be appropriate to use pairs of oligonucleotides on a microarray.
  • the “pairs” will be identical, except for one nucleotide which preferably is located in the center of the sequence.
  • the second oligonucleotide in the pair serves as a control.
  • the number of oligonucleotide pairs may range from two to one million.
  • the oligomers are synthesized at designated areas on a substrate using a light-directed chemical process.
  • the substrate may be paper, nylon or other type of membrane, filter, chip, glass slide or any other suitable solid support.
  • kits are provided that is useful for characterizing the skin of an individual, e.g., using the methods provided by the present invention to determine the age range characteristic of the skin of a subject.
  • a kit of the invention includes a skin sample collection device and one or more probes or primers that selectively bind to one or more of the nucleic acid molecules of Table 1, Table 2, Table 3, or any combination thereof.
  • the kit includes one or more applicators in addition to or instead of the skin sample collection device. Such applicators are useful for in situ analysis of gene expression on the skin of a subject. For example, an applicator may be used to apply detectably labeled probes for visual detection of expressed RNA to characterize the skin lesion.
  • a kit of the invention includes a probe that binds to a portion of a nucleic acid molecule in Table 1, Table 2, Table 3, or any combination thereof.
  • the kit further includes a microarray that contains at least a fragment of a gene or a nucleic acid molecule or a protein product of any one of the genes listed in Table 1, Table 2, Table 3, or any combination thereof.
  • many reagents may be provided in a kit of the invention, only some of which should be used together in a particular reaction or procedure. For example, multiple primers may be provided, only two of which are needed for a particular application.
  • the kit of the invention provides a compartmentalized carrier including a first container containing a pair of primers.
  • the primers are typically a forward primer that selectively binds upstream of a gene on one strand, and a reverse primer that selectively binds upstream of a gene on a complementary strand.
  • the kits of the present invention can further include an instruction insert, e.g., disclosing methods for sample collection using the sample collection device and/or exemplary gene expression profiles for comparison with the expression profile of the sample taken from the subject.
  • phase 1 the tape stripped specimens and biopsied sample collections were performed by the principal investigator or trained individuals delegated by the principal investigator to obtain the biopsy sample at various sites.
  • the RNA profiling phase includes, but is not limited to RNA purification and hybridization to DNA microarrays for gene expression profiling.
  • Adhesive tape was purchased from Adhesives Research (Glen Rock, Pa.) in bulk rolls. These rolls were custom fabricated into small circular discs, 17 millimeters in diameter, by Diagnostic Laminations Engineering (Oceanside, Calif.).
  • Human spleen total RNA was purchased from Ambion (catalogue # 7970; Austin, Tex.).
  • RNeasy RNA extraction kit was purchased from Qiagen (Valencia, Calif.).
  • Reverse transcriptase, PCR primers and probes, and TaqMan Universal Master Mix which included all buffers and enzymes necessary for the amplification and fluorescent detection of specific cDNAs, were purchased from Applied Biosystems (Foster City, Calif.).
  • MELT total nucleic acid isolation system was purchased from Ambion (Austin, Tex.).
  • RNA isolation was extracted from tapes using either pressure cycling technology (PCT; Garrett, Tao et al. 2002; Schumacher, Manak et al. 2002) or MELT total nucleic acid system. Tapes were extracted in pairs by insertion into a PULSETM tube (Pressure Biosciences, Gaithersburg, Md.) with 1.2 mls of buffer RLT (supplied in the Qiagen RNeasy kit). PULSETM tubes were inserted into the PCT-NEP2017 pressure cycler and the sample was extracted using the following parameters: room temperature; 5 pressure cycles of 35 Kpsi with pressure held for 20 seconds at the top and bottom of each cycle.
  • RNA from the 2 sites stripped on each subject was pooled to create a single sample from each subject.
  • RNA isolation using MELT total nucleic acid protocol Tapes were extracted in a 2 ml eppendorf tube with 192 ⁇ l MELT buffer plus 8 ⁇ l of MELT cocktail and vortexed for 10 minutes at room temperature. The MELT lysates were transferred to the dispensed binding bead master mix after spinning down for 3 minutes at >10,000 ⁇ g and washed with 300 ⁇ l of Wash Solution 1 and 2. RNAs were eluted in 100 ⁇ l of elution solution.
  • RNA mass recovered from tapes is determined by using quantitative RT-PCR with reference to a standard curve (C t, actin vs. log [RNA]; AppliedBiosystems 2001) created from commercially purchased human spleen total RNA. The average of 6 replicate C t, actin values was used to calculate the concentration of RNA in a sample with reference to the standard curve.
  • RNA amplification and array hybridization RNA was isolated by the Multi-Enzymatic Liquefaction of Tissue method (Ambion, Austin, Tex.) and amplified using the WT-Ovation pico amplification system (NuGen, San Carlos, Calif.). The amplified RNA was hybridized to Affymetrix U133 plus 2.0 microarray and data were processed and analyzed using R from Bioconductor.
  • Preprocessing GeneChip Data The image files from scanning the Affymetrix GeneChips with the Affymetrix series 3000 scanner will be converted using GCOS software (Affymetrix) to “CEL” format files. Normalization of CEL files will be carried out using software from the Bioconductor suite (on the world wide web at bioconductor.org). In particular, a robust multiarray analysis with adjustments for optical noise and binding affinities of oligonucleotide probes (Wu et al., 2006; and Wu et al., 2004) as implemented by the function “just.gcrma” in the “gcrma” package will be used to normalize the GeneChip Data.
  • classification rules will rely on resampling methods (k-fold cross-validation, the 632 plus bootstrap, and/or bagging applied to the naive Bayes classifier and the nearest shrunken centroid classifier and the support vector machine (SVM) which both performed well in classifying prostate tissues as malignant or benign, used in our previous work.
  • SVM support vector machine
  • the implementation likely to be used is to perform k-fold cross-validation.
  • an initial screen of the training data for differentially expressed genes is performed and genes are ordered according to their posterior probability of differential expression.
  • Naive Bayes and nearest shrunken centroid classifiers based on the genes with the highest posterior probability of differential expression are formed choosing enough values of r between 1 and 1024 to allow accurate interpolation of the classification error rate.
  • the “one se rule” is applied to the error rates for the test sets to choose the classifier that minimizes the error rate.
  • SVM an internal 632+ bootstrap is applied to each training sample to select the number of genes to be used in forming the classifier.
  • the “1 se rule” error rates from the k test sets are used to characterize the classification accuracy.
  • RNA, amplified cDNA and microarray data Following informed consent, the skin of subjects was tape stripped using EGIR. The resulting RNA isolated from the EGIR tape was amplified and profiled on the Affymetrix U133 plus 2.0 GeneChip. Microarray data were normalized by the GCRMA algorithm. To assure high quality of microarray data are generated, QC metrics were established for RNA, amplified cDNA and microarray data. The quality of RNA was assessed by capillary electrophoresis using the Experion system (Biorad, Hercule, Calif.) and RNA with at least one visible 18S rRNA was further processed for RNA amplification.
  • the amplified cDNA was quantified by the Nanodrop system and quality of the amplified cDNA was also assessed by the Experion system. The yield of the amplified cDNAs greater than 5 ⁇ g and the average size distribution of the cDNAs greater than 750 nt were carried forward for microarray hybridization. Quality of the array data was further assessed using simpleaffy program in R and the array data with scaling factor less than 5.0 and % present call greater than 30% were used for further data analysis.
  • the PAM software uses a modification of the nearest centroid method, which computes a standardized centroid for each class in a training set. This refers to the average gene expression for each gene in each class divided by the within-class standard deviation for that gene.
  • Nearest centroid classification takes the gene expression profile of a new sample, and compares it to each of these class centroids. The class, whose centroid it is closest to, in squared distance, is the predicted class for that new sample.
  • RNA harvested by EGIR technology is more than adequate for microarray-based gene expression profiling and appropriately reflects the pathologic state of skin.
  • the following procedure was used to recover nucleic acids from normal skin (e.g., the mastoid or upper back areas) of a subject.
  • Tapes were handled with gloved hands at all times. A particular site that is relatively blemish-free and healthy was located, unless otherwise specified by the protocol. Preferred normal skin sites are the mastoid process (the bony process behind the ear at the base of the skull) and the upper back, immediately superior to the scapular spine. Shave the site if necessary to remove non-vellus hairs. The site was cleansed with an alcohol wipe (70% isopropyl alcohol) and let air dry completely before application of the tape. The tape was then applied to the skin site. If more than one tape was used, application was in sequential order starting from the left side. A surgical skin marker and/or a water soluble marker was used to mark the location of the tape on the skin in order to align subsequent tapes.
  • Preferred normal skin sites are the mastoid process (the bony process behind the ear at the base of the skull) and the upper back, immediately superior to the scapular spine. Shave the site if necessary to remove non-vellus hairs. The site was cleansed
  • the tape harvesting procedure was started by applying pressure to the tape and ensuring that the skin was held taut to ensure that the tape does not move while applying pressure. The tape was then removed slowly in one direction. An edge of the tape was then placed onto the strip at the top of a packet with the adhesive surface of the tape facing down to protect the sample. Sequential tapes were then put on the same site, if applicable, and removed slowly in an opposite direction to that used in the immediately previous application.
  • the sites of application were stripped with a total of at least four tapes, unless otherwise specified in the protocol. Tapes were then put into a storage bag and immediately placed on dry ice or into storage at ⁇ 20° C. or below until analysis.

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WO2010025341A2 (fr) 2010-03-04
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AU2009285645A1 (en) 2010-03-04
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CN102177253A (zh) 2011-09-07
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